disappearing skin_vertices after assigning new mesh to object
When scripting updates to obj.data there currently (Jan 2016) does not seem to be a way to refresh data.skin_vertices without removing and adding the modifier. 

For example if the "SKIN" modifier is named "sv_skin"

    # if modifier present, remove
    if 'sv_skin' in obj.modifiers:
        sk = obj.modifiers['sv_skin']
        obj.modifiers.remove(sk)

    # make new modifier and get reference to it.
    a = obj.modifiers.new(type='SKIN', name='sv_skin')


If you have a few other items on that object's modifier stack then there's a bit more bookkeeping to do.

Here's an example of a working scripted update to generate a lattice mesh with a skin modifier in Sverchok.



The code: https://gist.github.com/zeffii/e556ebcb33737a3fd58b

  &lt;-- includes the script, but does require Sverchok.